Off-line two-dimensional reversed-phase liquid chromatography (2D-RPLC) coupled to electrospray ionization-ion trap mass spectrometry (ESI-ITMS) was operated in positive mode (PI) to characterize polymethoxylated flavonoids (PMFs) in botanical sample. The fragments of [M+H-nx15](+) produced by loss of one or more methyl group from the protonated molecules, as well as [M+H-14](+), [M+H-29](+), [M+H-33](+), [M+H-43](+), [M+H-46](+) and [M+H-61](+) fragments formed the Multiple MS (MS(n)) "fingerprint" of PMFs. 42 target compounds were tentatively identified from the extract of Fructus aurantii (F. aurontii) based on this "fingerprint". Experimental outcomes indicated that the application of 2D separation method can reduce the matrix suppression of analytes caused by the coelution with interferential components and the column overloading of interferential components. 42 versus 23 target compounds were detected through 2D versus 1 D method, which confirm the superiority of 2D coupled to MS in elimination of matrix effects. (c) 2008 Elsevier B.V. All rights reserved.